Re: [gmx-users] AFM pulling simulations
X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] AFM pulling simulations
http://www.gromacs.org/Documentation/Tutorials On 03/22/2011 11:02 AM, X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, -- Laura Kingsley Graduate Student Medicinal Chemistry and Molecular Pharmacology Purdue University Office: RHPH 504A 575 Stadium Mall Dr. West Lafayette, IN 47907 Office Phone: (765) 496-6643 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] AFM pulling simulations
Thanks Justin, That is pretty much the only tutorial one can found. I have one question now, how do I force a particular orientation of my protein during genbox (for example if i need to pull along N-C vector, i need my protein oriented that way, i.e in Z direction for example to later apply the force in that direction). Date: Tue, 22 Mar 2011 11:15:54 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] AFM pulling simulations X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] AFM pulling simulations
too eager to send an email.. I think playing with editconf with princ flag should do the trick .. sorry folks and thanks for the help !! From: xru...@live.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] AFM pulling simulations Date: Tue, 22 Mar 2011 15:47:41 + Thanks Justin, That is pretty much the only tutorial one can found. I have one question now, how do I force a particular orientation of my protein during genbox (for example if i need to pull along N-C vector, i need my protein oriented that way, i.e in Z direction for example to later apply the force in that direction). Date: Tue, 22 Mar 2011 11:15:54 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] AFM pulling simulations X Rules wrote: Hello All, I am looking for a very simple (step-by-step) tutorial on AFM pulling simulations (constant force/ constant velocity) with gromacs. Can someone point me to a simple tutorial to perform these simulations with gromacs? Thanks, http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] AFM Pulling Simulations
On 26/08/10 19:56, chris.ne...@utoronto.ca wrote: Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period of time, then the stage is set for frustration and ultimate disaster. Lots of people think that these things are plug and play -- of course, they are not. If you don't have a mentor nearby who can help you, then figuring this all out and getting some meaningful data could easily take you a year. I don't mean to scare you off, but it is true that while no professor asks a new student to get protein crystals within a few months, that request is often made for simulation results from experimental supervisors. Perhaps the gromacs community should be working toward getting testimonials to the significant amount of time that it can take to learn to run simulations properly on the gromacs site that new users could direct their supervisors to in the case that those supervisors are not acquainted with molecular simulation. I couldn't agree more. I have been thrown into learning GROMACS and designing a coarse grain model from scratch (my background is that of an experimentalist, doing AFM pulling experiments, by the way!), all practically by myself. I mean: I *wanted* to learn all of that, I just didn't expect I would have done it *alone*. So I read the Frenkel-Smit book, the GROMACS manual, and banged my head a lot (luckly I was already experienced with Linux and programming). No wonder one year after, I'm just beginning to see where I am going *sigh*. m. Chris. Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AFM Pulling Simulations
Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] AFM Pulling Simulations
Quoting Justin A. Lemkul jalem...@vt.edu: Natalie Stephenson wrote: Hi, I'm a complete novice when it comes to using any kind of command prompt based programmes and hadn't even heard of Linux until my supervisor wanted me to use gromacs ... so needless to say I'm running into a few problems!! I've managed to perform all the generic energy minimisations etc on my protein (basically I can do everything that has been spoon fed to me on the tutorial), but now I want to begin simulating AFM pulling experiments. I've printed (and bound!) the entire manual but I'm still coming up against problems with understanding how I go about running the AFM simulations. Does anyone have a basic syntax they have used to perform a similar simulation so I can work from there and figure out what I need to put where? Also, do I need to create any specific input files for these simulations? Thanks so much for your help with this... A rather inept gromacs user (Natalie!) xxx There is a steered MD component to the umbrella sampling tutorial: http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling Though it is an excellent reference, the manual will not teach you everything you need to know. The mailing list archive (although currently glitching) and Google are your friends, as well. There are hundreds of threads in the archive about pull code success and failure, at least some of which should be informative :) Thanks loads!! I'll give it a try! Natalie xxx -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
